scPDB - 1xbt entry

Protein Data Bank Entry:

PDB ID : 1xbt

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2004-08-31

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Thymidine kinase, cytosolic
ID:	KITH_HUMAN
AC:	P04183
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.7.1.21

Chains:

Chain Name:	Percentage of Residues within binding site
G	97 %
H	3 %

Ligand binding site composition:

B-Factor:	33.361
Number of residues:	40
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.275	513.000

% Hydrophobic	% Polar
44.74	55.26
According to VolSite

Ligand :

HET Code:	TTP
Formula:	C10H13N2O14P3
Molecular weight:	478.137 g/mol
DrugBank ID:	DB02452
Buried Surface Area:	80.18 %
Polar Surface area:	279.44 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	2
Rings:	2
Aromatic rings:	0
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
23.4769	38.0627	-3.147

Binding mode :

What is Poseview ?

2D View
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Image generated by PoseView

Protein

Binding Site

Ligand

Interaction pattern

hydrophobic (CA)

aromatic (CZ)

hydrogen bond acceptor (O)

hydrogen bond acceptor/donor (OG)

hydrogen bond donor (N)

positively ionized (NZ)

negatively ionized (OD1)

metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT

Ligand	Protein		Interaction
Atom	Atom	Residue	Distance (Å)	Angle (°)	Type
C2'	SD	MET- 28	3.85	0	Hydrophobic	false
C5M	SD	MET- 28	4.41	0	Hydrophobic	false
C3'	CE	MET- 28	3.68	0	Hydrophobic	false
O3B	N	PHE- 29	3.01	152.46	H-Bond (Protein Donor)	false
O2G	N	GLY- 31	2.99	133.44	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 32	2.85	156.31	H-Bond (Protein Donor)	false
O3G	NZ	LYS- 32	2.8	160.55	H-Bond (Protein Donor)	false
O3G	N	LYS- 32	2.94	157.88	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 32	2.85	0	Ionic (Protein Cationic)	false
O3G	NZ	LYS- 32	2.8	0	Ionic (Protein Cationic)	false
O1G	N	SER- 33	3.49	164.45	H-Bond (Protein Donor)	false
O3'	OD2	ASP- 58	2.7	143.67	H-Bond (Ligand Donor)	false
C4'	CE1	PHE- 101	4.06	0	Hydrophobic	false
C1'	CZ	PHE- 101	3.78	0	Hydrophobic	false
C5'	CD2	LEU- 124	3.8	0	Hydrophobic	false
C5M	CD2	LEU- 124	3.8	0	Hydrophobic	false
O4	N	PHE- 128	3	146.61	H-Bond (Protein Donor)	false
C5M	CB	THR- 163	3.86	0	Hydrophobic	false
N3	O	VAL- 172	2.68	163.6	H-Bond (Ligand Donor)	false
O2	N	VAL- 174	2.98	141.59	H-Bond (Protein Donor)	false
O3'	N	GLY- 176	3.45	170.71	H-Bond (Protein Donor)	false
C5M	CE2	TYR- 181	3.87	0	Hydrophobic	false
C2'	CE1	TYR- 181	3.59	0	Hydrophobic	false
O1A	MG	MG- 7194	2.03	0	Metal Acceptor	false
O1B	MG	MG- 7194	2.26	0	Metal Acceptor	false
O1G	MG	MG- 7194	2.04	0	Metal Acceptor	false
O2A	O	HOH- 7216	2.92	179.96	H-Bond (Protein Donor)	false